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Mathematical modelling is an important tool for understanding the dynamics of the spread of infectious diseases, which could be the result of a natural outbreak or of the intentional release of pathogenic biological agents. Decision makers and policymakers responsible for strategies to contain disease, prevent epidemics and fight possible bioterrorism attacks, need accurate computational tools, based on mathematical modelling, for preventing or even managing these complex situations. In this article, we tested the validity, and demonstrate the reliability, of an open-source software, the Spatio-Temporal Epidemiological Modeler (STEM), designed to help scientists and public health officials to evaluate and create models of emerging infectious diseases, analysing three real cases of Ebola haemorrhagic fever (EHF) outbreaks: Uganda (2000), Gabon (2001) and Guinea (2014). We discuss the cases analysed through the simulation results obtained with STEM in order to demonstrate the capability of this software in helping decision makers plan interventions in case of biological emergencies. [ABSTRACT FROM AUTHOR]